Aetiology of severe community acquired pneumonia in adults identified by combined detection methods: a multi-centre prospective study in China

ABSTRACT

Severe Community Acquired Pneumonia (SCAP) challenges public health globally. Considerable improvements in molecular pathogen testing emerged in the last few years. Our prospective study combinedly used traditional culture, antigen tests, PCR and mNGS in SCAP pathogen identification with clinical outcomes. From June 2018 to December 2019, we conducted a multi-centre prospective study in 17 hospitals of SCAP patients within 48 hours of emergency room stay or hospitalization in China. All clinical data were uploaded into an online database. Blood, urine and respiratory specimens were collected for routine culture, antigen detection, PCR and mNGS as designed appropriately. Aetiology confirmation was made by the local attending physician group and scientific committee according to microbiological results, clinical features, and response to the treatment. Two hundred seventy-five patients were included for final analysis. Combined detection methods made identification rate up to 74.2% (222/299), while 14.4% (43/299) when only using routine cultures and 40.8% (122/299) when not using mNGS. Influenza virus (23.2%, 46/198), S. pneumoniae (19.6%, 39/198), Enterobacteriaceae (14.6%, 29/198), Legionella pneumophila (12.6%, 25/198), Mycoplasma pneumoniae (11.1%, 22/198) were the top five common pathogens. The in-hospital mortality of patients with pathogen identified and unidentified was 21.7% (43/198) and 25.9% (20/77), respectively. In conclusion, early combined detection increased the pathogen identification rate and possibly benefitted survival. Influenza virus, S. pneumoniae, Enterobacteriaceae was the leading cause of SCAP in China, and there was a clear seasonal distribution pattern of influenza viruses. Physicians should be aware of the emergence of uncommon pathogens, including Chlamydia Psittaci and Leptospira.

Keywords:

• Severe community acquired pneumonia
• mNGS
• combined detection
• multi-centre study
• Chlamydia Psittaci

Acknowledgements

We thank all the patients who participated in this study, the clinical site investigators (Zhao JY, Shi MM, Jiao Y, Liang S, Zhou F, Shang LH, Wang QY, Cheng Q, Zhang T, Liu JX, Li RR, Li X, Wang GD, Zhang YQ, Rui YW, Zhang L, Xu LN, Zhang SN, Yao YK, Jiang YQ et al.), and Zuo Ming from Ruijin Hospital who maintained the online database. We also thank Zhejiang Medicine, who helped in logistics.

Disclosure statement

No potential conflict of interest was reported by the author(s).

Additional information

Funding

This work was supported by Severe Pneumonia Cohort and Biological Sample Data Repository (SHDC2020CR5010), Cultivation Project of Shanghai Major Infectious Disease Research Base (20dz2210500), Key Laboratory of Emergency Prevention, Diagnosis and Treatment of Respiratory Infectious Diseases, Shanghai (20dz2261100), and National Innovative Research Team of High-level Local Universities in Shanghai